[gmx-users] Protein-ligand

[Justin Lemkul]

On 4/19/17 8:40 AM, RAHUL SURESH wrote:
> Dear Justin,
> Thank you
>
> But What do you mean my appropriate energygrps.? Protein ligand.? Will that
> give interaction energy between ligand and protein.?

Yes.

-Justin

> On Wed, 19 Apr 2017 at 5:17 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 4/19/17 6:50 AM, RAHUL SURESH wrote:
>>> Dear Gromacs users
>>>
>>> how to determine the interaction energy between ligand and protein at
>> each
>>> frame of simulation?
>>>
>>
>> Set appropriate energygrps in the .mdp file, create a new .tpr and use
>> mdrun
>> -rerun to recalculate the interaction energies from the existing
>> trajectory.
>> This quantity may or may not be physically meaningful, depending on the
>> details
>> of the force field.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================